19-40764993-GTCGTTC-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_004596.5(SNRPA):c.690-12_690-7delGTTCTC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000292 in 1,546,968 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_004596.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNRPA | ENST00000243563.8 | c.690-14_690-9delTCGTTC | intron_variant | Intron 5 of 5 | 1 | NM_004596.5 | ENSP00000243563.2 | |||
SNRPA | ENST00000601393.1 | c.627-14_627-9delTCGTTC | intron_variant | Intron 5 of 5 | 3 | ENSP00000472355.1 | ||||
SNRPA | ENST00000601545.5 | c.540-14_540-9delTCGTTC | intron_variant | Intron 5 of 5 | 5 | ENSP00000470534.1 | ||||
SNRPA | ENST00000596860.1 | n.136-14_136-9delTCGTTC | intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00150 AC: 229AN: 152216Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000502 AC: 99AN: 197204Hom.: 0 AF XY: 0.000376 AC XY: 40AN XY: 106438
GnomAD4 exome AF: 0.000160 AC: 223AN: 1394634Hom.: 0 AF XY: 0.000139 AC XY: 96AN XY: 689850
GnomAD4 genome AF: 0.00150 AC: 229AN: 152334Hom.: 1 Cov.: 32 AF XY: 0.00138 AC XY: 103AN XY: 74488
ClinVar
Submissions by phenotype
SNRPA-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at